@computingnature

group leader @HHMIJanelia | diversity + open-science for better science | she/her | VOTE BLUE Mostly on MASTODON: @Computingnature@neuromatch.social, join us!

 Ashburn, VA
mouseland.github.io/
Joined June 2016
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Did you vote today!?!?!? Polls were busy in #virginia this morning! FYI #virginia has same day voter registration! elections.virginia.gov/regis…
Harris walz kaine and suhas for Virginia!

ALT Harris walz kaine and suhas for Virginia!

Kamala will cut taxes for 100 million Americans

ALT Kamala will cut taxes for 100 million Americans

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📢 #Rastermap paper out now, easily explore and visualize your neural recordings 🐭🐒🐟 and ANNs 🤖 nature.com/articles/s41593-0…. Updates from preprint include analyses of primate data and IBL task data. Video tutorial: youtu.be/oQHq7yUWn2k #Neuroscience #MachineLearning
Carsen Stringer @[email protected]@computingnature29 Jul 2023
Make your next discovery using #Rastermap, a visualization method for large-scale neural data. Paper now out, w/ @marius10p : biorxiv.org/content/10.1101/…
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Spike sorting with #Kilosort in #python w/ #pytorch + @pyqtgraph ! >>> pip install kilosort[gui] To learn more, check out the docs (kilosort.readthedocs.io/en/l… by Jacob Pennington), or watch the talk (youtube.com/watch?v=LTSmoACr… by @marius10p )
Marius Pachitariu@marius10p9 Apr 2024
The Kilosort4 paper is now published @naturemethods. We put a lot of work into building and properly documenting all things Kilosort (including for older versions). w/ @computingnature #kilosort paper: nature.com/articles/s41592-0… code: github.com/MouseLand/Kilosor…
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Replying to @computingnature @Redklavier
However, we recommend our "super-generalist" cyto3 model as it has been trained on more datasets from even more imaging modalities (github.com/MouseLand/cellpos…)
segmentations of "cyto3" Cellpose model in yellow, ground-truth in purple

ALT segmentations of "cyto3" Cellpose model in yellow, ground-truth in purple

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#Cellpose remains the state-of-the-art for cellular segmentation. See our new paper, in response to Ma et al, Nat Methods 2024. Paper: biorxiv.org/content/10.1101/… Leaderboard results ⬇️⬇️⬇️
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Check out our lab’s recent work on visual learning and representations at the #cosyne24 #cosyne2024 workshops:
Neural correlates of behavior in novel sensory contexts, Mon Mar 4 @ 15:30, Sala II; Unsupervised pretraining in biological neural networks, Mon Mar 4 @ 17:10, Sala I; Towards a simplified model of primary visual cortex, Tues Mar 5 @ 10:15, Sala XV

ALT Neural correlates of behavior in novel sensory contexts, Mon Mar 4 @ 15:30, Sala II; Unsupervised pretraining in biological neural networks, Mon Mar 4 @ 17:10, Sala I; Towards a simplified model of primary visual cortex, Tues Mar 5 @ 10:15, Sala XV

Marius Pachitariu@marius10p3 Mar 2024
Add these workshop sessions to your agenda to see recent work from the Pachitariu-Stringer lab at #cosyne24: whova.com/portal/webapp/cosy… whova.com/portal/webapp/cosy… whova.com/portal/webapp/cosy… Work by @NunezKant , @Lin_Zhong_ion , @FarahDu6 and @computingnature.
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Replying to @computingnature @marius10p
or for upsampling
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Replying to @computingnature @marius10p
you can also use Cellpose3 for deblurring
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#Cellpose 3! Not all images are perfect. Restore your images with Cellpose3 to get better segmentations, w/ @marius10p biorxiv.org/content/10.1101/…
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all presentations from the lab, exploring behavioral and visual responses in cortex: #SfN23 #SfN2023
Beverly Setzer: Sat 11/11 1PM HH8 - The relationship between behavior and fMRI dynamics in the thalamus is state dependent Lin Zhong: Sun 11/12 8:45 AM @ WCC 147A - Supervised and unsupervised learning of neural representations for visual generalization Atika Syeda: Sun 11/12 8AM Y4 - Facemap: a framework for modeling neural activity based on orofacial tracking Judith Hoeller: Sun 11/12 8AM W19 - How populations of neurons in visual cortex encode perspective Carsen Stringer: Sun 11/12 8AM Y6 - Disentangling sensory, motor and cognitive variables with Rastermap Miguel Nunez: Tues 11/14 8AM DD15 - Generalization from one exemplar in mice Jacob Pennington: Tues 11/14 1PM XX57 - Solving the spike sorting problem with Kilosort Fengtong Du: Wed 11/15 8AM XX10 - A simplified model of high-dimensional neural responses to stimuli Qingqing Zhang: Wed 11/15 1PM EE25 - Visual sequence prediction in superficial visual cortex

ALT Beverly Setzer: Sat 11/11 1PM HH8 - The relationship between behavior and fMRI dynamics in the thalamus is state dependent Lin Zhong: Sun 11/12 8:45 AM @ WCC 147A - Supervised and unsupervised learning of neural representations for visual generalization Atika Syeda: Sun 11/12 8AM Y4 - Facemap: a framework for modeling neural activity based on orofacial tracking Judith Hoeller: Sun 11/12 8AM W19 - How populations of neurons in visual cortex encode perspective Carsen Stringer: Sun 11/12 8AM Y6 - Disentangling sensory, motor and cognitive variables with Rastermap Miguel Nunez: Tues 11/14 8AM DD15 - Generalization from one exemplar in mice Jacob Pennington: Tues 11/14 1PM XX57 - Solving the spike sorting problem with Kilosort Fengtong Du: Wed 11/15 8AM XX10 - A simplified model of high-dimensional neural responses to stimuli Qingqing Zhang: Wed 11/15 1PM EE25 - Visual sequence prediction in superficial visual cortex

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Our lab is presenting at #SfN23 #SfN2023 see all presentation times here! mouseland.github.io/#news Sun AM visit posters Y4 + Y6 to get free stickers and pins #opensource
Stickers for our open source software facemap, kilosort and cellpose, and a suite2p pin

ALT Stickers for our open source software facemap, kilosort and cellpose, and a suite2p pin

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